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protocols::forge::components::BDR Class Reference

#include <BDR.hh>

Inheritance diagram for protocols::forge::components::BDR:
Inheritance graph
[legend]

Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::forge::build::BuildInstructionOP 
BuildInstructionOP
 
typedef
protocols::forge::build::BuildManager 
BuildManager
 
typedef
protocols::forge::build::BuildManager::Original2Modified 
Original2Modified
 
typedef
protocols::forge::build::Interval 
Interval
 
typedef protocols::moves::MoverOP MoverOP
 
typedef std::pair< Interval,
String
OriginalInterval2DesignString
 A pair storing a instruction's original interval and a string denoting the sequence during design. More...
 
typedef utility::vector1
< OriginalInterval2DesignString
DesignInfo
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 BDR ()
 default constructor More...
 
 BDR (BDR const &rval)
 copy constructor More...
 
 ~BDR () override
 default destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
bool use_fullmer () const
 use full-mer fragments when building the loop? (default false) More...
 
bool use_sequence_bias () const
 use sequence biased fragments when building the loop? (default false) More...
 
Real max_linear_chainbreak () const
 the maximum allowed linear chainbreak (default 0.07) More...
 
String const & centroid_loop_mover_str () const
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool redesign_loop_neighborhood () const
 redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...
 
String const & resfile () const
 name of the resfile to use during design-refine; empty string implies no resfile More...
 
core::Size dr_cycles () const
 the number of design-refine cycles to perform, default 3 More...
 
ScoreFunction const & centroid_scorefunction () const
 the centroid level score function, default "remodel_cen" More...
 
ScoreFunction const & fullatom_scorefunction () const
 the full-atom level score function, default score12 More...
 
void add_instruction (BuildInstructionOP bi, String const &aa_during_design_refine=String())
 add instruction to the manager of this BDR (no copy) More...
 
void create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v)
 create directed dependency between two instructions More...
 
void use_fullmer (bool const flag)
 use full-mer fragments when building the loop? More...
 
void use_sequence_bias (bool const flag)
 use sequence biased fragments when building the loop? (default false) More...
 
void max_linear_chainbreak (Real const threshold)
 the maximum allowed linear chainbreak More...
 
void centroid_loop_mover_str (String const &loop_mover_str)
 the loop mover string to use during centroid build More...
 
void redesign_loop_neighborhood (bool const flag)
 redesign the neighborhood around the loop? if false, then just repacks during the design phase More...
 
void resfile (String const &filename)
 name of the resfile to use during design-refine; empty string implies no resfile More...
 
void dr_cycles (core::Size const cycles)
 set the number of design-refine cycles to perform More...
 
void centroid_scorefunction (ScoreFunction const &sfx)
 set the centroid level score function More...
 
void centroid_scorefunction (ScoreFunctionOP sfx)
 set the centroid level score function More...
 
void fullatom_scorefunction (ScoreFunction const &sfx)
 set the full-atom level score function More...
 
void fullatom_scorefunction (ScoreFunctionOP sfx)
 set the full-atom level score function More...
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static String neighborhood_calc_name ()
 the name for the loops' neighborhood calculator More...
 
static String loops_buns_polar_calc_name ()
 the name for the loops' buried unsatisfied polars calculator More...
 
static String neighborhood_buns_polar_calc_name ()
 the name for the loops' neighborhood buried unsatisfied polars calculator More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

BDRoperator= (BDR const &rval)
 copy assignment More...
 
bool centroid_build (Pose &pose)
 run the centroid level build stage More...
 
bool design_refine (Pose &pose)
 run the design-refine stage More...
 
TaskFactoryOP generic_taskfactory ()
 return a TaskFactory useable as a starting point for either design or refinement More...
 
void process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a continuous design string, adding appropriate operations to the TaskFactory More...
 
void process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a design string containing an insert, adding appropriate operations to the TaskFactory More...
 

Static Private Member Functions

static utility::vector1< bool >
const & 
allowed_surface_aa ()
 return a boolean vector specifying allowed a.a. when designing on the surface More...
 

Private Attributes

BuildManager manager_
 the BuildManager More...
 
DesignInfo design_info_
 Stores instructions' original interval and a string denoting the sequence during design. More...
 
bool use_fullmer_
 use full-mer fragments when building the loop? (default false) More...
 
bool use_sequence_bias_
 use sequence biased fragments when building the loop? (default false) More...
 
Real max_linear_chainbreak_
 the maximum allowed linear chainbreak (default 0.07) More...
 
String centroid_loop_mover_str_
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool redesign_loop_neighborhood_
 redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...
 
String resfile_
 name of the resfile to use during design-refine; empty string implies no resfile More...
 
core::Size dr_cycles_
 the number of design-refine cycles to perform, default 3 More...
 
ScoreFunctionOP centroid_sfx_
 the centroid scorefunction to use, default "remodel_cen" More...
 
ScoreFunctionOP fullatom_sfx_
 the full-atom scorefunction to use, default score12 More...
 
VarLengthBuildOP vlb_
 VLB for centroid_build. More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Member Typedef Documentation

A pair storing a instruction's original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

Constructor & Destructor Documentation

protocols::forge::components::BDR::BDR ( )

default constructor

protocols::forge::components::BDR::BDR ( BDR const &  rval)

copy constructor

References vlb_.

protocols::forge::components::BDR::~BDR ( )
overridedefault

default destructor

Member Function Documentation

void protocols::forge::components::BDR::add_instruction ( BuildInstructionOP  bi,
String const &  aa_during_design_refine = String() 
)

add instruction to the manager of this BDR (no copy)

Parameters
[in]biBuildInstruction
[in]aa_during_design_refineThe allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert
[in]biBuildInstruction
[in]aa_during_design_refineThe allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly. Default empty string.

References protocols::forge::build::BuildManager::add(), design_info_, manager_, and vlb_.

utility::vector1< bool > const & protocols::forge::components::BDR::allowed_surface_aa ( )
staticprivate

return a boolean vector specifying allowed a.a. when designing on the surface

References core::chemical::aa_from_oneletter_code().

Referenced by process_continuous_design_string(), and process_insert_design_string().

void protocols::forge::components::BDR::apply ( Pose pose)
overridevirtual
bool protocols::forge::components::BDR::centroid_build ( Pose pose)
private
String const& protocols::forge::components::BDR::centroid_loop_mover_str ( ) const
inline

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

void protocols::forge::components::BDR::centroid_loop_mover_str ( String const &  loop_mover_str)
inline

the loop mover string to use during centroid build

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

BDR::ScoreFunction const & protocols::forge::components::BDR::centroid_scorefunction ( ) const

the centroid level score function, default "remodel_cen"

References centroid_sfx_.

void protocols::forge::components::BDR::centroid_scorefunction ( ScoreFunction const &  sfx)

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

void protocols::forge::components::BDR::centroid_scorefunction ( ScoreFunctionOP  sfx)

set the centroid level score function

References centroid_sfx_.

BDR::MoverOP protocols::forge::components::BDR::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

void protocols::forge::components::BDR::create_directed_dependency ( BuildInstructionOP  u,
BuildInstructionOP  v 
)

create directed dependency between two instructions

References protocols::forge::build::BuildManager::create_directed_dependency(), and manager_.

bool protocols::forge::components::BDR::design_refine ( Pose pose)
private
core::Size protocols::forge::components::BDR::dr_cycles ( ) const
inline

the number of design-refine cycles to perform, default 3

References dr_cycles_.

void protocols::forge::components::BDR::dr_cycles ( core::Size const  cycles)
inline

set the number of design-refine cycles to perform

Remarks
set this to 0 to skip design-refine

References dr_cycles_.

BDR::MoverOP protocols::forge::components::BDR::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

BDR::ScoreFunction const & protocols::forge::components::BDR::fullatom_scorefunction ( ) const

the full-atom level score function, default score12

the full-atom level score function

References fullatom_sfx_.

void protocols::forge::components::BDR::fullatom_scorefunction ( ScoreFunction const &  sfx)

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

void protocols::forge::components::BDR::fullatom_scorefunction ( ScoreFunctionOP  sfx)

set the full-atom level score function

References fullatom_sfx_.

BDR::TaskFactoryOP protocols::forge::components::BDR::generic_taskfactory ( )
private

return a TaskFactory useable as a starting point for either design or refinement

References resfile_.

Referenced by design_refine().

std::string protocols::forge::components::BDR::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

static String protocols::forge::components::BDR::loops_buns_polar_calc_name ( )
inlinestatic

the name for the loops' buried unsatisfied polars calculator

Referenced by apply().

Real protocols::forge::components::BDR::max_linear_chainbreak ( ) const
inline

the maximum allowed linear chainbreak (default 0.07)

References max_linear_chainbreak_.

void protocols::forge::components::BDR::max_linear_chainbreak ( Real const  threshold)
inline

the maximum allowed linear chainbreak

References max_linear_chainbreak_.

static String protocols::forge::components::BDR::neighborhood_buns_polar_calc_name ( )
inlinestatic

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::components::BDR::neighborhood_calc_name ( )
inlinestatic

the name for the loops' neighborhood calculator

Referenced by apply(), and design_refine().

BDR& protocols::forge::components::BDR::operator= ( BDR const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::forge::components::BDR::process_continuous_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private

process a continuous design string, adding appropriate operations to the TaskFactory

References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), and protocols::forge::build::Interval::left.

Referenced by design_refine().

void protocols::forge::components::BDR::process_insert_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private
bool protocols::forge::components::BDR::redesign_loop_neighborhood ( ) const
inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

References redesign_loop_neighborhood_.

void protocols::forge::components::BDR::redesign_loop_neighborhood ( bool const  flag)
inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase

References redesign_loop_neighborhood_.

String const& protocols::forge::components::BDR::resfile ( ) const
inline

name of the resfile to use during design-refine; empty string implies no resfile

References resfile_.

void protocols::forge::components::BDR::resfile ( String const &  filename)
inline

name of the resfile to use during design-refine; empty string implies no resfile

References protocols::abinitio::filename(), and resfile_.

bool protocols::forge::components::BDR::use_fullmer ( ) const
inline

use full-mer fragments when building the loop? (default false)

References use_fullmer_.

void protocols::forge::components::BDR::use_fullmer ( bool const  flag)
inline

use full-mer fragments when building the loop?

References use_fullmer_.

bool protocols::forge::components::BDR::use_sequence_bias ( ) const
inline

use sequence biased fragments when building the loop? (default false)

References use_sequence_bias_.

void protocols::forge::components::BDR::use_sequence_bias ( bool const  flag)
inline

use sequence biased fragments when building the loop? (default false)

References use_sequence_bias_.

Member Data Documentation

String protocols::forge::components::BDR::centroid_loop_mover_str_
private

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

Referenced by centroid_build(), and centroid_loop_mover_str().

ScoreFunctionOP protocols::forge::components::BDR::centroid_sfx_
private

the centroid scorefunction to use, default "remodel_cen"

Referenced by centroid_build(), and centroid_scorefunction().

DesignInfo protocols::forge::components::BDR::design_info_
private

Stores instructions' original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

Referenced by add_instruction(), and design_refine().

core::Size protocols::forge::components::BDR::dr_cycles_
private

the number of design-refine cycles to perform, default 3

Referenced by apply(), design_refine(), and dr_cycles().

ScoreFunctionOP protocols::forge::components::BDR::fullatom_sfx_
private

the full-atom scorefunction to use, default score12

Referenced by design_refine(), and fullatom_scorefunction().

BuildManager protocols::forge::components::BDR::manager_
private
Real protocols::forge::components::BDR::max_linear_chainbreak_
private

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), design_refine(), and max_linear_chainbreak().

bool protocols::forge::components::BDR::redesign_loop_neighborhood_
private

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

Referenced by design_refine(), and redesign_loop_neighborhood().

String protocols::forge::components::BDR::resfile_
private

name of the resfile to use during design-refine; empty string implies no resfile

Referenced by generic_taskfactory(), and resfile().

bool protocols::forge::components::BDR::use_fullmer_
private

use full-mer fragments when building the loop? (default false)

Referenced by centroid_build(), and use_fullmer().

bool protocols::forge::components::BDR::use_sequence_bias_
private

use sequence biased fragments when building the loop? (default false)

Referenced by centroid_build(), and use_sequence_bias().

VarLengthBuildOP protocols::forge::components::BDR::vlb_
private

VLB for centroid_build.

Remarks
Store it here instead of re-instantiation each centroid_build() call so fragment caching works.
Warning
Remember to set this to null if the BuildManager changes.

Referenced by add_instruction(), BDR(), and centroid_build().


The documentation for this class was generated from the following files: